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acekingman2000
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Joined: 10/1/2001
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String alignment as proposed by Needleman and Wunch aims to minimise the edit distance from string one to string two where the edit distance is the sequence of inserts/deletes to convert string one to string two. The operations of match, insert and delete are given a cost such as 0 for a match and ?V1 for an insert /delete. The string with the least cost describes the alignment. The algorithm described by Needleman and Wunch is recursive and NOT the one you will implement given that you are using shell scripts.
My Problem is that how do you use "Windows Scripting Host with Vbscript under Windows" to create such a script.
I have to write the script such that it accepts two strings of characters made up of the letters A,C,G,T. The string can be up to 20 characters long. For example,
stringX= gaacgtaggcgtat and stringY=ATACTACGGAGGG would have an optimal alignment GAACGTAGGCGTAT
Write the script such that it accepts two strings of characters made up of the letters A,C,G,T. The string can be up to 20 characters long. For example,
stringX= gaacgtaggcgtat and stringY=ATACTACGGAGGG would have an optimal alignment GAACGTAGGCGTAT ATACT_ACGGAGG_G
Some suggest that my algorithm should be in the form of:
Initialisation
?K.
For I = I to length(stringX)
?K..
For J = 1 to length(stringY)
If stringX[I]=stringY[J] then
Match
?K.
Else
Mismatch
?K..
endif
next J
?K.
Next I
Your output should be the list of the possible alignments in cost order. You may use utilities like sort and head for the Unix case. For the Windows case, write the results to an excel spreadsheet, sort the columns and find the minimum value.
Can anyone here help with my problem with VBScript and UNIX's C Shell Scripting?
Thank you
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